Re: r25603 - /trunk/lib/spectrum/nmrpipe.py -- September 04, 2014 - 11:06

Hi Troels,

This also looks good, but needs a whitespace fix for the '=' sign.
For the RelaxError, I would also capitalise the P in Python, as Python
is always with a capitial P and this is the start of a sentence.  It
is also better to use a single sentence for the RelaxError when
possible:

RelaxError:  Python module 'subprocess' not found, cannot call showApod.

I would suggest also changing the logic at the start to be:

"""
if not dep_check.subprocess_module:
    raise RelaxError("Python...
"""

Then you don't need to indent the rest and the code is hence simpler.
You could also add a check of 'if not dep_check.showApod:" to give a
RelaxError when showApod is not available.

Cheers,

Edward


On 3 September 2014 22:50,  <tlinnet@xxxxxxxxxxxxx> wrote:
> Author: tlinnet
> Date: Wed Sep  3 22:50:33 2014
> New Revision: 25603
>
> URL: http://svn.gna.org/viewcvs/relax?rev=25603&view=rev
> Log:
> To the lib function of spectrum.nmrpipe, added function to call the NMRPipe 
> program showApod, to get the output from the program.
>
> Modified:
>     trunk/lib/spectrum/nmrpipe.py
>
> Modified: trunk/lib/spectrum/nmrpipe.py
> URL: 
> http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=25603&r1=25602&r2=25603&view=diff
> ==============================================================================
> --- trunk/lib/spectrum/nmrpipe.py       (original)
> +++ trunk/lib/spectrum/nmrpipe.py       Wed Sep  3 22:50:33 2014
> @@ -28,8 +28,14 @@
>  from warnings import warn
>
>  # relax module imports.
> +import dep_check
>  from lib.errors import RelaxError
> +from lib.io import get_file_path
>  from lib.warnings import RelaxWarning
> +
> +# Check subprocess is available.
> +if dep_check.subprocess_module:
> +    import subprocess
>
>
>  def read_seriestab(peak_list=None, file_data=None, int_col=None):
> @@ -185,3 +191,35 @@
>
>          # Add the assignment to the peak list object.
>          peak_list.add(res_nums=[res_num1, res_num2], res_names=[res_name1, 
> res_name2], spin_names=[name1, name2], shifts=[w1, w2], 
> intensity=intensities, intensity_name=spectra)
> +
> +
> +def show_apod_extract(file_name=None, dir=None, 
> path_to_command='showApod'):
> +    """Extract showApod information for spectrum fourier transformed with 
> NMRPipe.
> +
> +    @keyword file:              The filename of the NMRPipe fourier 
> transformed file.
> +    @type file:                 str
> +    @keyword dir:               The directory where the file is located.
> +    @type dir:                  str
> +    @keyword path_to_command:   If showApod not in PATH, then specify 
> absolute path as: /path/to/showApod
> +    @type dir:                  str
> +    @return:                    The output from showApod as list of lines.
> +    @rtype:                     list of lines
> +    """
> +
> +    # Get the file path.
> +    file_path = get_file_path(file_name=file_name, dir=dir)
> +
> +    if dep_check.subprocess_module:
> +        # Call function.
> +        Temp=subprocess.Popen([path_to_command, file_path], 
> stdout=subprocess.PIPE)
> +
> +        # Communicate with program, and get outout and exitcode.
> +        (output, errput) = Temp.communicate()
> +
> +        # Wait for finish and get return code.
> +        return_value = Temp.wait()
> +
> +        return output.splitlines()
> +
> +    else:
> +        raise RelaxError("python module 'subprocess' not found.  Cannot 
> call showApod.")
>
>
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